CanvasBin.CanvasBin.LoadObservedAlignmentsBAM C# (CSharp) Method

        static void LoadObservedAlignmentsBAM(string bamFile, bool isPairedEnd, string chromosome, CanvasCoverageMode coverageMode, HitArray observed, Int16[] fragmentLengths)
        {
            // Sanity check: The .bai file must exist, in order for us to seek to our target chromosome!
            string indexPath = bamFile + ".bai";
            if (!File.Exists(indexPath))
            {
                throw new Exception(string.Format("Fatal error: Bam index not found at {0}", indexPath));
            }

            using (BamReader reader = new BamReader(bamFile))
            {
                int desiredRefIndex = -1;
                desiredRefIndex = reader.GetReferenceIndex(chromosome);
                if (desiredRefIndex == -1)
                {
                    throw new ApplicationException(
                        string.Format("Unable to retrieve the reference sequence index for {0} in {1}.", chromosome,
                        bamFile));
                }
                bool result = reader.Jump(desiredRefIndex, 0);
                if (!result)
                {
                    // Note: This is not necessarily an error, it just means that there *are* no reads for this chromosome in this
                    // .bam file.  That is not uncommon e.g. for truseq amplicon.
                    return;
                }
                int readCount = 0;
                int keptReadCount = 0;
                string header = reader.GetHeader();
                BamAlignment alignment = new BamAlignment();
                while (reader.GetNextAlignment(ref alignment, true))
                {
                    readCount++;

                    // Flag check - Require reads to be aligned, passing filter, non-duplicate:
                    if (!alignment.IsMapped()) continue;
                    if (alignment.IsFailedQC()) continue;
                    if (alignment.IsDuplicate()) continue;
                    if (alignment.IsReverseStrand()) continue;
                    if (!alignment.IsMainAlignment()) continue;

                    // Require the alignment to start with 35 bases of non-indel:
                    if (alignment.CigarData[0].Type != 'M' || alignment.CigarData[0].Length < 35) continue;

                    if (isPairedEnd && !alignment.IsProperPair()) continue;

                    int refID = alignment.RefID;

                    // quit if the current reference index is different from the desired reference index
                    if (refID != desiredRefIndex)
                        break;

                    if (refID == -1)
                        continue;

                    keptReadCount++;
                    if (coverageMode == CanvasCoverageMode.Binary)
                    {
                        observed.Data[alignment.Position] = 1;
                    }
                    else
                    {
                        observed.Set(alignment.Position);
                    }
                    // store fragment size, make sure it's within Int16 range and is positive (simplification for now)
                    if (coverageMode == CanvasCoverageMode.GCContentWeighted)
                        fragmentLengths[alignment.Position] = Convert.ToInt16(Math.Max(Math.Min(Int16.MaxValue, alignment.FragmentLength), 0));
                }
                Console.WriteLine("Kept {0} of {1} total reads", keptReadCount, readCount);
            }
        }